First commit to the reproduction pipeline template

Let's start working on this pipeline independently with this first
commit. It is based on my previous experiences, but I had never made a
skeleton of a pipeline before, it was always within a working analysis.

But now that the pipeline has a separate repository for its self, we will
be able to work on it and use it as a base for future work and modify it to
make it even better. Hopefully in time (and with the help of others), it
will grow and become much more robust and useful.

20 files changed, 1465 insertions, 0 deletions

diff --git a/.dir-locals.el b/.dir-locals.el
new file mode 100644
index 0000000..af98cc8
--- /dev/null
+++ b/.dir-locals.el
@@ -0,0 +1,20 @@
+;; This files contains Emacs Directory Local Variables.
+;;
+;; Emacs is an extensible, customizable, free/libre text editor.  It
+;; allows specification of certain settings that will be applied to
+;; all files in current directory and its subdirectories. This is
+;; useful in order to automatically enforce certain coding conventions
+;; for all contributors of Gnuastro, like the maximum length of lines
+;; or the number of spaces to be used for indentation.
+;;
+;; For more information see (info "(emacs) Directory Variables")
+
+((nil
+  (indent-tabs-mode . nil) ;; No tabs as indentation
+  (fill-column . 75))      ;; 75-character wide lines
+ (c-mode
+  (c-basic-offset . 2)     ;; 2 spaces of indentation
+  (c-file-style . "gnu"))  ;; GNU style for braces
+ (makefile-mode
+  (indent-tabs-mode . t))  ;; Real TABs are important in makefiles
+ )
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..cb41e68
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,14 @@
+*~
+*.txt
+*.aux
+*.log
+*.pdf
+*.out
+*.auxlock
+config/mmap_*
+
+reproduce/build
+reproduce/BDIR/
+tex/pipeline.tex
+reproduce/SURVEY/
+reproduce/config/pipeline/DIRECTORIES.mk
\ No newline at end of file
diff --git a/.gnuastro b/.gnuastro
new file mode 120000
index 0000000..5ccb4fd
--- /dev/null
+++ b/.gnuastro
@@ -0,0 +1 @@
+reproduce/config/gnuastro
\ No newline at end of file
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..357a2e0
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,110 @@
+# A ONE-LINE DESCRIPTION OF THE WHOLE PIPELINE
+#
+# Original author:
+#     Your name <your@email.address>
+# Contributing author(s):
+# Copyright (C) YYYY, Your Name.
+#
+# This Makefile is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# Ultimate target of this pipeline
+# --------------------------------
+#
+# The final paper (in PDF format) is the main target of this whole
+# reproduction pipeline. So as defined in the Make paradigm, we are
+# defining it as the first target.
+#
+# Note that if you don't have LaTeX to build the PDF or generally are just
+# interested in the processing, you can avoid the skip to create the final
+# PDF, see `reproduce/config/pipeline/pdf.mk'.
+all: paper.pdf
+
+
+
+
+
+# Include specific Makefiles
+# --------------------------
+#
+# To keep things clean, managable and readable, each set of operations is
+# (and must be) classified (modularized) by context into separate
+# Makefiles: the more the better. They are included in this top-level
+# Makefile through the command below.
+#
+# To further help in readability, it is best to avoid including Makefiles
+# within any other Makefile. So in short, it is best that the `foreach'
+# loop below contains all the `reproduce/src/make/*.mk' files.
+#
+# IMPORTANT NOTE: order matters in the inclusion of the processing
+# Makefiles. As the pipeline grows, some Makefiles will probably define
+# variables/dependencies that others need. Therefore unlike the
+# `reproduce/config/pipeline/*.mk' Makefiles which only define low-level
+# variables (not dependent on other variables and contain no rules), the
+# high-level processing Makefiles are included through the `foreach' loop
+# below by explicitly requesting them in a specific order here.
+include reproduce/config/pipeline/*.mk
+include $(foreach f, initialize download paper, reproduce/src/make/$(f).mk)
+
+
+
+
+
+# LaTeX macros for paper
+# ----------------------
+#
+# The final report's PDF (final target of this reproduction pipeline) takes
+# variable strings from the pipeline. Those variables are defined as LaTeX
+# macros in `tex/pipeline.tex'. This file is thus the interface between the
+# pipeline scripts and the final PDF.
+#
+# Each of the pipeline steps will save their macros into their own `.tex'
+# file in the `$(mtexdir)' directory. Those individual macros are the
+# pre-requisite to `tex/pipeline.txt'. `tex/pipeline.tex' is thus a
+# high-level output and is defined in this top-most Makefile (and not
+# `reproduce/src/make/paper.mk'). This enables a clear demonstration of the
+# top-level dependencies clearly.
+#
+# The symbolic link to the build directory (`bdirsym') is also placed here
+# as a dependency if the pipeline is to be created. It is very important
+# that it be an "order-only prerequisite" (after a `|', otherwise, it will
+# try to be remade on every call and `ln' will complain and abort).
+#
+# Note that if you don't want the final PDF and just want the processing
+# and file outputs, you can remove the value of the `pdf-compile' variable
+# in `reproduce/config/pipeline/pdf.mk'.
+tex/pipeline.tex: $(foreach f, initialize download, $(mtexdir)/$(f).tex)   \
+                  | $(bdirsym)
+
+        # If no PDF is requested, then just exit here.
+ifeq ($(pdf-compile),)
+	@echo;
+	@echo "Everything is OK until this point, but not building PDF."
+	@echo "To do so, give a value to the 'pdf-compile' variable."
+	@echo;
+	@exit 1
+endif
+
+        # Read all the separate files and put them into the final TeX
+        # macros file. Since `bdirsym' maybe empty, we can't use the
+        # `filter-out' function generically. We'll have to check `bdirsym'
+        # first.
+ifeq ($(bdirsym),)
+	cat $^ > $@
+else
+	cat $(filter-out $(bdirsym),$^) > $@
+endif
diff --git a/README b/README
new file mode 100644
index 0000000..95b53b6
--- /dev/null
+++ b/README
@@ -0,0 +1,153 @@
+Reproduction pipeline for XXXXX.
+
+For a general introduction to reproducible science as done here,
+please see the link below:
+
+  http://akhlaghi.org/reproducible-science.html
+
+
+
+Running the pipeline
+====================
+
+To reproduce the results, please take these steps in order:
+
+1. Make sure you have the dependencies (below).
+
+2. Edit `reproduce/config/pipeline/DIRECTORIES.mk'.
+
+   This file keeps the important top-level directories for this
+   pipeline in your system. Open it with a text editor and give the
+   necessary locations. The comments in this file (lines starting with
+   a `#') should help in understanding the purpose of each directory.
+
+   In short, if you don't have the input files on your system, this
+   pipeline will download them in the specified directory. Also, the
+   intermediate/build directory may be relatively large (~1GB), so
+   please choose a build location with sufficient space.
+
+3. Run the following command to reproduce everything on 8 threads. If
+   your CPU has a different number of threads, change the number.
+
+     $ make -j8
+
+
+
+Output
+======
+
+The output of the pipeline is a PDF file, describing the published
+paper.
+
+
+
+Dependencies
+============
+
+To reproduce the results you need the following programs. Except for
+Gnuastro, the version of the other programs will not make a
+difference.
+
+  Gnuastro Y.Y
+  ------------
+
+  Gnuastro is a large collection of programs for astronomical data
+  analysis on the command-line. This is an intermediate version of
+  Gnuastro (the tarball is not officially released on the Gnuastro
+  webpage). However, this pipeline will ONLY work with this version of
+  Gnuastro. For convenience, this tarball is available in the
+  following link:
+
+    https://zenodo.org/record/ZZZZZZ/files/gnuastro-Y.Y.tar.gz
+
+  To uncompress, build and install the Gnuastro tarball, follow the
+  instructions in the link below.
+
+    https://www.gnu.org/software/gnuastro/manual/html_node/Quick-start.html
+
+  If you successfully downloaded the tarball from the link above,
+  please ignore the rest of this section on Gnuastro. If not, this
+  version of Gnuastro is always present in Gnuastro's version
+  controlled history and this reproduction pipeline contains the fix
+  to implement to it.
+
+  To build the above version of Gnuastro, please clone Gnuastro and
+  checkout this version as shown in the following commands:
+
+    $ git clone http://git.sv.gnu.org/r/gnuastro.git
+    $ git checkout Y.Y
+
+  Afterwords, you need to bootstrap Gnuastro as described in the
+  following link.
+
+    https://www.gnu.org/software/gnuastro/manual/html_node/Bootstrapping.html
+
+  You are now ready to configure, build and install Gnuastro as
+  described in the "Quick start" link above.
+
+
+
+  AWK
+  ---
+
+  AWK is a program for working with text files. GNU AWK is the most
+  common implementation and it is commonly already installed on most
+  systems.
+
+
+  GNU Make
+  --------
+
+  This reproduction pipeline uses some features that may not be
+  present in other implementations of Make.
+
+
+  flock
+  -----
+
+  This is a small program to manage file locks from the
+  command-line. It is available in most GNU/Linux distributions.
+
+  If you can't find it in your package manager or on some Mac OS
+  systems, please put a copy of `reproduce/src/flock' file into your
+  search path (this script needs Perl, so have that installed is
+  well). To learn more about the search path and where to install this
+  file, please see the link below. Before running this pipeline you
+  should be able to run the `flock' command on your command-line.
+
+    https://www.gnu.org/software/gnuastro/manual/html_node/Installation-directory.html
+
+
+  Wget or cURL
+  ------------
+
+  These programs (`wget' or `curl' on the command-line) are used to
+  download the input files if you don't already have them.
+
+
+  Tar and Gzip
+  ------------
+
+  Tar is used for packaging multiple files into one and Gzip is used
+  for compression. They are both very common software in Unix-like
+  operating systems, so they are probably already available on your
+  system.
+
+
+  GNU Coreutils
+  -------------
+
+  Very basic command-line programs (for example `cp' or `mkdir'). They
+  may be implemented differently in non-GNU systems (for example Mac
+  OS). But have not actually been tested in Mac OS. Alternatively,
+  there are ways to install Coreutils on Mac OS (for example with
+  Homebrew), please do a search to find solutions. Please get in touch
+  with us if any errors occur due to such basic programs.
+
+
+  LaTeX
+  -----
+
+  LaTeX is used to build the final PDF of this pipeline. Some
+  important packages within LaTeX that this pipeline uses are:
+  `biblatex' and `pgfplots'.
diff --git a/README.md b/README.md
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index 0000000..1a52571
--- /dev/null
+++ b/README.md
@@ -0,0 +1,400 @@
+Introduction
+============
+
+This description is for *creators* of the reproduction pipeline. See
+`README` on instructions for running it.
+
+This project contains a **fully working template** for a high-level
+research reproduction pipeline as defined in the link below. If this page
+is inaccessible at the time of reading, please see the end of this file
+which contains a portion of the introduction in this webpage.
+
+  http://akhlaghi.org/reproducible-science.html
+
+This template is created with the aim of supporting reproducible research
+by making it easy to start a project in this framework. It is very easy to
+customize this template pipeline for any particular research/job and expand
+it as it starts and evolves. It can be run with no modification (as
+described in `README`) as a demonstration and customized by editing the
+existing rules and adding new rules as well as adding new Makefiles as the
+research/project grows.
+
+This file will continue with a discussion of why Make is the perfect
+language/framework for a research reproduction pipeline and how to master
+Make easily. Afterwards, a checklist of actions that are necessary to
+customize this pipeline for your research is provided. The main body of
+this text will finish with some tips and guidelines on how to manage or
+extend it as your research grows. Please share your thoughts and
+suggestions on this pipeline so we can implement them and make it even more
+easier to use and more robust.
+
+
+Why Make?
+---------
+
+When batch processing is necessary (no manual intervention, as in a
+reproduction pipeline), shell scripts are usually the first solution that
+comes to mind. However, the problem with scripts for a scientific
+reproduction pipeline is the complexity and non-linearity. A script will
+start from the top/start every time it is run. So if you have gone through
+90% of a research project and want to run the remaining 10% that you have
+newly added, you have to run the whole script from the start again and wait
+until you see the effects of the last few steps (for the possible errors,
+or better solutions and etc). It is possible to manually ignore/comment
+parts of a script to only do a special part, but such checks/comments will
+only add to the complexity of the script and they is prone to very serious
+bugs in the end (when trying to reproduce from scratch). Such bugs are very
+hard to notice when adding the checks or commenting-code in a script.
+
+The Make paradigm, on the other hand, starts from the end: the final
+target. It builds a dependency tree internally, and finds where it should
+actually start each time it is run. Therefore, in the scenario above, a
+researcher that has just added the final 10% of steps of her research to
+her Makefile, will only have run those extra steps. As commonly happens in
+a research context, due to its paradigm Make, it is also trivial to change
+the processing of any intermediate (already written) rule/step in the
+middle of an already written pipeline: the next time Make is run, only
+rules affected by the changes/additions will be re-run.
+
+This greatly speeds up the processing (enabling creative changes), while
+keeping all the dependencies clearly documented (as part of the Make
+language), and most importantly, enabling full reproducibility from scratch
+with no changes in the pipeline code that was working during the
+research. Since the dependencies are also clearly demarcated, Make can
+identify independent steps and run them in parallel (further speeding up
+the process). Make was designed for this purpose and it is how huge
+projects like all Unix-like operating systems (including GNU/Linux or Mac
+OS operating systems) and their core components are built. Therefore, Make
+is a highly mature paradigm/system with robust and highly efficient
+implementations in various operating systems perfectly suited for a complex
+non-linear research project.
+
+Make is a small language with the aim of defining "rules" containing
+"targets", "prerequisites" and "recipes". It comes with some cool features
+like functions or automatic-variables to greatly facilitate the management
+of any of those constructs. For a more detailed (yet still general)
+introduction see Wikipedia:
+
+  https://en.wikipedia.org/wiki/Make_(software)
+
+Many implementations of Make exist and all should be usable with this
+pipeline. This pipeline has been created and tested mainly with GNU Make
+which is the most common implementation. But if you see parts specific to
+GNU Make, please inform us to correct it.
+
+
+How can I learn Make?
+---------------------
+
+The best place to learn Make from scratch is the GNU Make manual. It is an
+excellent and non-technical (in its first chapters) book to help get
+started. It is freely available and always up to date with the current
+release. It also clearly explains which features are specific to GNU Make
+and which are general in all implementations. So the first few chapters
+regarding the generalities are useful for all implementations.
+
+The first link below has links to the GNU Make manual in various formats
+and in the second, you can get it in PDF (which may be easier to read in
+the first time).
+
+  https://www.gnu.org/software/make/manual/
+
+  https://www.gnu.org/software/make/manual/make.pdf
+
+If you use GNU Make, you also have the whole GNU Make manual on the
+command-line with the following command (you can come out of the "info"
+environment by pressing `q`, if you don't know "Info", we strongly
+recommend running "$ info info" to learn it easily, it greatly simplifies
+your access to many manuals that are installed on your system).
+
+```shell
+  $ info make
+```
+
+If you use the Emacs text editor, you will find the Info version of the
+Make manual there also.
+
+
+
+
+Checklist to customize the pipeline
+===================================
+
+Take the following steps to fully customize this pipeline for your research
+project. After finishing the list, be sure to run `./configure` and `make`
+to see if everything works correctly before expanding it. If you notice
+anything missing or any in-correct part (probably a change that has not
+been explained here), please let us know to correct it.
+
+ - **Get this repository** (if you don't already have it): Arguably the
+     easiest way to start is to clone this repository as shown below:
+
+     ```shell
+     $ git clone https://gitlab.com/makhlaghi/reproduction-pipeline-template.git
+     ```
+
+ - **Copyright**, **name** and **date**: Go over the following files and
+     correct the copyright, names and dates in their first few lines:
+     `README`, `Makefile` and `reproduce/src/make/*.mk`. When making new
+     files, always remember to add a similar copyright statement at the top
+     of the tile.
+
+ - **Gnuastro**: GNU Astronomy Utilities (Gnuastro) is currently a
+     dependency of the pipeline and without it, the pipeline will complain
+     and abort. The main reason for this is to demonstrate how critically
+     important it is to version your software. If you don't want to install
+     Gnuastro please follow the instructions in the list below. If you do
+     have Gnuastro (or have installed it to check this pipeline), then
+     after an initial check, try un-commenting the `onlyversion` line and
+     running the pipeline to see the respective error. Such features in a
+     software makes it easy to design a robust pipeline like this. If you
+     have tried it and don't need Gnuastro in your pipeline, also follow
+     this list:
+
+   - Delete the description about Gnuastro in `README`.
+   - Delete everything about Gnuastro in `reproduce/src/make/initialize.mk`
+   - Delete `and Gnuastro \gnuastrover` from `tex/preamble-style`
+
+ - **Initiate a new Git repo**: You don't want to mix the history of this
+     template reproduction pipeline with your own reproduction
+     pipeline. You have already made some small changes in the previous
+     step, so let's re-initiate history before continuing. But before doing
+     that, keep the output of `git describe` in a place and write it in
+     your first commit message to document what point in this pipeline's
+     history you started from. Since the pipeline is highly integrated with
+     your particular research, it may not be easy to merge the changes
+     later. Having the commit in this history that you started from, will
+     allow you to check and manually apply any changes that don't interfere
+     with your implemented pipeline. After this step, you can commit your
+     changes into your newly initiated history as you like.
+
+     ```shell
+     $ git describe          # The point in this history you started from.
+     $ git clean -fxd        # Remove any possibly created extra files.
+     $ rm -rf .git           # Completely remove this history.
+     $ git init              # Initiate a new history.
+     $ git add --all         # Stage everything that is here.
+     $ git commit            # Make your first commit (mention the first output)
+     ```
+
+ - **`README`**: Go through this top-level instruction file and make it fit
+     to your pipeline: update the text and etc. Don't forget that your
+     colleagues or anyone else, will first be drawn to read this file, so
+     make it as easy as possible for them to understand your
+     work. Therefore, also check and update `README` one last time when you
+     are ready to publish your work (and its reproduction pipeline).
+
+ - **First input dataset**: The user manages the top-level directory of the
+     input data through the variables set in
+     `reproduce/config/pipeline/DIRECTORIES.mk.in` (the user actually edits
+     a `DIRECTORIES.mk` file that is copied from the `.mk.in` file, but the
+     `.mk` file is not under version control). So open this file and
+     replace `SURVEY` with the name of your input survey or dataset (all in
+     capital letters), for example if you are working on data from the XDF
+     survey, replace `SURVEY` with `XDF`. But don't change the value, just
+     the name. Afterwards, change any occurrence of `SURVEY` in the whole
+     pipeline with the new name. You can find the occurrences with a simple
+     command like the ones shown below. We follow the Make convention here
+     that all `ONLY-CAPITAL` variables are those directly set by the user
+     and all `small-caps` variables are set by the pipeline designer. All
+     variables that also depend on this survey have a `survey` in their
+     name. Hence, also correct all these occurrences to your new name in
+     small-caps. Of course, ignore those occurrences that are irrelevant,
+     like those in this file. Note that in the raw version of this template
+     no target depends on these files, so they are ignored. Afterwards, set
+     the webpage and correct the filenames in
+     `reproduce/src/make/download.mk' if necessary.
+
+     ```shell
+     $ grep -r SURVEY ./
+     $ grep -r survey ./
+     ```
+
+ - **Other input datasets**: Add any other input datasets that may be
+     necessary for your research to the pipeline based on the example
+     above.
+
+
+Tips on using the pipeline
+==========================
+
+The following is a list of points, tips, or recommendations that have been
+learned after some experience with this pipeline. Please don't hesitate to
+share any experience you gain after using this pipeline with us. In this
+way, we can add it here for others to also benefit.
+
+ - **Modularity**: Modularity is the key to easy and clean growth of a
+     project. So it is always best to break up a job into as many
+     sub-components as reasonable. Here are some tips to stay modular.
+
+   - *Short recipes*: if you see the recipe of a rule becoming more than a
+      few lines, it probably a good sign that you should break up the job.
+
+   - *Context-based (many) Makefiles*: This pipeline is designed to allow
+      the easy inclusion of many Makefiles (in `reproduce/src/make/*.mk`)
+      for maximal modularity. So keep the rules for closely related parts
+      of the processing in separate Makefiles.
+
+   - *Clear file names*: Be very clear and descriptive with the naming of
+      the files and the variables because a few months after the processing
+      it will be very hard to remember what each one does. Also this helps
+      others (your collaborators or other people reading the pipeline after
+      it is published) to more easily understand your work and find their
+      way around.
+
+   - *Standard naming*: As the project grows, following a good standard in
+      naming the files is very useful. Try best to use multiple word
+      filenames for anything that is non-trivial (separating the words with
+      a `-`). For example if you have a Makefile for creating a catalog and
+      another two for processing it under models A and B, you can name them
+      like this: `catalog-create.mk`, `catalog-modela.mk` and
+      `catalog-modelb.mk`. In this way, when listing the contents of
+      `reproduce/src/make` to see all the Makefiles, those related to the
+      catalog will all be close to each other and thus easily found. This
+      also helps in auto-completions by the shell or text editors like
+      Emacs.
+
+   - *Source directories*: If you need to add scripts (shell, Python, AWK
+      or any other language), keep them in a separate directory under
+      `reproduce/src`, with the appropriate name.
+
+   - *Configuration files*: If your research uses special programs as part
+      of the processing, put all their configuration files in a devoted
+      directory (with the program's name) within
+      `reproduce/config`. Similar to the `reproduce/config/gnuastro`
+      directory (which is put in the template as a demo in case you use GNU
+      Astronomy Utilities). It is much cleaner and readable (thus less
+      buggy) to avoid mixing the configuration files, even if there is no
+      technical necessity.
+
+
+ - **Contents**: It is good practice to follow the following
+     recommendations on the contents of your files, whether they are source
+     code for a program, Makefiles, scripts or configuration files
+     (copyrights aren't necessary for the latter).
+
+   - *Copyright*: Always start a file containing programming constructs
+      with a copyright statement like the ones that this template starts
+      with (for example in the top level `Makefile`).
+
+   - *Comments*: Comments are vital for readability (by yourself in two
+      months or others). Describe everything you can about why you are
+      doing something, how you are doing it, and what you expect the result
+      to be. Write the comments as if it was what you would say to describe
+      the variable, recipe or rule to a friend sitting beside you. When
+      writing the pipeline it is very tempting to just steam ahead, but be
+      patient and write comments before the rules or recipes. This will
+      also allow you to think more about what you should be doing. Also, in
+      several months when you come back to the code, you will appreciate
+      the effort of writing them. Just don't forget to also read and update
+      the comment first if you later want to make changes to the variable,
+      recipe or rule. As a general rule of thumb: first the comments, then
+      the code.
+
+
+ - **Make programming**: Here are some experiences that we have come to
+     learn over the years in using Make and are useful/handy in research
+     contexts.
+
+   - *Automatic variables*: These are wonderful and very useful Make
+      constructs that greatly shrink the text, while help in read-ability,
+      robustness (less bugs in typos for example) and generalization. For
+      example even when a rule only has one target or one prerequisite,
+      always use `$@` instead of the target's name, `$<` instead of the
+      first prerequisite, `$^` instead of the full list of prerequisites
+      and etc. You can see the full list of automatic variables
+      [here](https://www.gnu.org/software/make/manual/html_node/Automatic-Variables.html). If
+      you use GNU Make, you can also see this page on your command-line:
+
+        ```shell
+        $ info make "automatic variables
+        ```
+
+   - *Large files*: If you are dealing with very large files (thus having
+      multiple copies of them for intermediate steps is not possible), one
+      solution is the following strategy. Set a small plain text file as
+      the actual target and delete the large file when it is no longer
+      needed by the pipeline (in the last rule that needs it). Below is a
+      simple demonstration of doing this, where we use Gnuastro's
+      Arithmetic program to add all pixels of the input image with 2 and
+      create `large1.fits`. We then subtract 2 from `large1.fits` to create
+      `large2.fits` and delete `large1.fits` in the same rule (when its no
+      longer needed). We can later do the same with `large2.fits` when it
+      is no longer needed and so on.
+        ```
+        large1.fits.txt: input.fits
+                astarithmetic $< 2 + --output=$(subst .txt,,$@)
+                echo "done" > $@
+        large2.fits.txt: large1.fits.txt
+                astarithmetic $(subst .txt,,$<) 2 - --output=$(subst .txt,,$@)
+                rm $(subst .txt,,$<)
+                echo "done" > $@
+        ```
+     A more advanced Make programmer will use [Make's call
+     function](https://www.gnu.org/software/make/manual/html_node/Call-Function.html)
+     to define a wrapper in `reproduce/src/make/initialize.mk`. This
+     wrapper will replace `$(subst .txt,,XXXXX)`. Therefore, it will be
+     possible to greatly simplify this repetitive statement and make the
+     code even more readable throughout the whole pipeline.
+
+
+ - **Dependencies**: It is critically important to exactly document, keep
+   and check the versions of the programs you are using in the pipeline.
+
+   - *Check versions*: In `reproduce/src/make/initialize.mk`, check the
+      versions of the programs you are using.
+
+   - *Keep the source tarball of dependencies*: keep a tarball of the
+      necessary version of all your dependencies (and also a copy of the
+      higher-level libraries they depend on). Software evolves very fast
+      and only in a few years, a feature might be changed or removed from
+      the mainstream version or the software server might go down. To be
+      safe, keep a copy of the tarballs (they are hardly ever over a few
+      megabytes, very insignificant compared to the data). If you intend to
+      release the pipeline in a place like Zenodo, then you can create your
+      submission early (before public release) and upload/keep all the
+      necessary tarballs (and data) there.
+
+   - *Keep your input data*: The input data is also critical to the
+      pipeline, so like the above for software, make sure you have a backup
+      of them
+
+
+
+
+
+
+
+Appendix: Introduction to this concept from link above
+======================================================
+
+In case [the link above](http://akhlaghi.org/reproducible-science.html) is
+not accessible at the time of reading, here is a copy of the introduction
+of that link, describing the necessity for a reproduction pipeline like
+this (copied on February 7th, 2018):
+
+The most important element of a "scientific" statement/result is the fact
+that others should be able to falsify it. The Tsunami of data that has
+engulfed astronomers in the last two decades, combined with faster
+processors and faster internet connections has made it much more easier to
+obtain a result. However, these factors have also increased the complexity
+of a scientific analysis, such that it is no longer possible to describe
+all the steps of an analysis in the published paper. Citing this
+difficulty, many authors suffice to describing the generalities of their
+analysis in their papers.
+
+However, It is impossible to falsify (or even study) a result if you can't
+exactly reproduce it. The complexity of modern science makes it vitally
+important to exactly reproduce the final result. Because even a small
+deviation can be due to many different parts of an analysis. Nature is
+already a black box which we are trying so hard to comprehend. Not letting
+other scientists see the exact steps taken to reach a result, or not
+allowing them to modify it (do experiments on it) is a self-imposed black
+box, which only exacerbates our ignorance.
+
+Other scientists should be able to reproduce, check and experiment on the
+results of anything that is to carry the "scientific" label. Any result
+that is not reproducible (due to incomplete information by the author) is
+not scientific: the readers have to have faith in the subjective experience
+of the authors in the very important choice of configuration values and
+order of operations: this is contrary to the scientific spirit.
\ No newline at end of file
diff --git a/configure b/configure
new file mode 100755
index 0000000..be18c25
--- /dev/null
+++ b/configure
@@ -0,0 +1,88 @@
+#! /bin/sh
+#
+# Necessary preparations/configurations for the reproduction pipeline.
+#
+# Original author:
+#     Your name <your@email.address>
+# Contributing author(s):
+# Copyright (C) YYYY, Your Name.
+#
+# This script is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This script is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# Location of the settings directory:
+pdir=reproduce/config/pipeline
+
+
+# Message to print for editing
+function msg {
+    echo; echo "Top-level reproduction directories are set.";
+    echo "Please run the following command to start the pipeline:"
+    echo "(Replace '8' with the number of CPU threads available)"
+    echo; echo "    make -j8"
+    echo;
+}
+
+
+# If `DIRECTORIES.mk' is already created, then ignore this step.
+if [ -f $pdir/DIRECTORIES.mk ]; then
+    echo
+    echo "$pdir/DIRECTORIES.mk already exists."
+    echo "To change/correct the top-level directories, please remove/edit it manually."
+    echo
+else
+
+    # Copy the base file to the desired output file.
+    if cp $pdir/DIRECTORIES.mk.in $pdir/DIRECTORIES.mk; then
+
+        # Tell the user to edit the directories.
+        while [ "$userread" != "y" -a "$userread" != "n" ]
+        do
+            echo "Top-level directories..."
+            echo
+            echo "These directories define the input(s) location and the"
+            echo "directory to host the intermediate/processing files."
+            echo
+            echo "To help in your ability to read and manage this pipeline,"
+            echo "it is recommended (but not mandatory) to change them to"
+            echo "a directory outside this reproduction pipeline."
+            echo
+            echo "More descriptions are provided within the file that is"
+            echo "opened if you choose to edit the directories."
+            echo
+            read -p"Edit the default top-level directories (y/n)? " userread
+        done
+
+        # Only continue if the user wants to edit the top level
+        # directories
+        if [ $userread = "y" ]; then
+
+            # Open a text editor to set the given directories
+            if emacs $pdir/DIRECTORIES.mk;   then msg
+            elif gedit $pdir/DIRECTORIES.mk; then msg
+            elif vi $pdir/DIRECTORIES.mk;    then msg
+            else
+                echo
+                echo "No common text editor found on your system."
+                echo "Please set the values in '$pdir/DIRECTORIES.mk' manually."
+                echo
+            fi
+        fi
+    else
+        echo; echo "Couldn't create $pdir/DIRECTORIES.mk"
+    fi
+fi
diff --git a/paper.tex b/paper.tex
new file mode 100644
index 0000000..8cf9cef
--- /dev/null
+++ b/paper.tex
@@ -0,0 +1,19 @@
+\documentclass{article}
+
+%% Necessary LaTeX preambles to include for relevant functionality. We
+%% don't want to start this file as fast as possible with the actual body
+%% of the report, while keeping modularity in the preambles.
+\input{tex/pipeline.tex}
+\input{tex/preamble-style.tex}
+%\input{tex/preamble-biblatex.tex}
+%\input{tex/preamble-pgfplots.tex}
+\input{tex/preamble-necessary.tex}
+
+%% Start writing.
+\begin{document}
+
+\maketitle
+
+Data were taken from \url{\websurvey}.
+
+\end{document}
diff --git a/reproduce/config/gnuastro/gnuastro.conf b/reproduce/config/gnuastro/gnuastro.conf
new file mode 100644
index 0000000..49f9906
--- /dev/null
+++ b/reproduce/config/gnuastro/gnuastro.conf
@@ -0,0 +1,36 @@
+# Default values for the common options to all the programs in GNU
+# Astronomy Utitlies.
+#
+# IMPORTANT NOTE FOR THE REPRODUCTION PIPELINE: The `lastconfig'
+# option is very important here, because we don't want any of
+# Gnuastro's programs to go into an un-controlled environment (user or
+# system wide configuration files). Uncomment the `onlyversion' option
+# when the paper/pipeline is ready to be published and set the value
+# of X.X accordingly.
+#
+# The rest of this configuration file in this template reproduction
+# pipeline is taken from the default Gnuastro configuration from its
+# source (`bin/gnuastro.conf').
+
+# Reproduction pipeline
+ lastconfig       1
+# onlyversion     X.X
+
+# Input:
+ hdu              1
+ ignorecase       1
+ searchin         name
+
+# Tessellation
+ tilesize         50,50
+ numchannels      1,1
+ remainderfrac    0.1
+ workoverch       0
+ interpnumngb     9
+ interponlyblank  0
+
+# Output:
+ tableformat      fits-binary
+
+# Operating mode
+ minmapsize       1000000000
\ No newline at end of file
diff --git a/reproduce/config/pipeline/DIRECTORIES.mk.in b/reproduce/config/pipeline/DIRECTORIES.mk.in
new file mode 100644
index 0000000..9ebd67b
--- /dev/null
+++ b/reproduce/config/pipeline/DIRECTORIES.mk.in
@@ -0,0 +1,50 @@
+# Top-level user specific directories. Note the points below:
+#
+# - The VALUES to these directories are initially JUST PLACE-HOLDERS!
+#   Please correct them based on your system.
+#
+# - The directories don't need to necessarily exist. If they do not exist,
+#   they will be created and the necessary data will be downloaded into
+#   them. Ofcourse provided that you have write permissions and an internet
+#   connection.
+#
+# - Do not use the tilde expansion `~' or variables for your home
+#   directory. Please use the full address, for example
+#   `/home/your-user-name'.
+#
+# - An ending forward-slash `/' is NOT necessary. In the pipeline, all
+#   these variables will be followed by a `/', so if you put a `/' at the
+#   end of the value here, you will see a `//' in the printed outputs
+#   during the processing. This has no technical problem, but can make
+#   reading the outputs harder and is thus not recommended.
+
+
+
+
+
+# Input data directories
+# ----------------------
+#
+# This is where the input data (with the same file-name standard as the
+# online webpage) are stored. If this directory doesn't exist, or it
+# doesn't contain the files (with the correct file-name formats), it will
+# be created and the images will be downloaded. See
+# `reproduce/config/pipeline/web.mk', for the URLs containing the expected
+# inputs for each survey.
+SURVEY = reproduce/SURVEY
+
+
+
+
+
+# Build directory
+# ---------------
+#
+# This is where the intermediate outputs of each step are kept.
+#
+# Why a separate build directory? So the source and configuration files for
+# this reproduction pipeline do not get crowded by all the
+# intermediate/derivative files. Also to make synchronization and backups
+# more easy: the contents of the build directory do not need to be backed
+# up since they can be reproduced and they can be large.
+BDIR = reproduce/BDIR
diff --git a/reproduce/config/pipeline/filters.mk b/reproduce/config/pipeline/filters.mk
new file mode 100644
index 0000000..6fa785d
--- /dev/null
+++ b/reproduce/config/pipeline/filters.mk
@@ -0,0 +1,25 @@
+# `filters' are the possible different parts of the survey, for
+# example filters in broad or narrow-band astronomical imaging
+# datasets. Since a generic term for them (to apply other types of
+# surveys/datasets) hasn't been considered yet, we'll stick with the
+# `filters' name. But feel free to correct it (or propose a
+# suggestion).
+#
+# If your dataset only has a single filter, or this concept is not
+# defined for your type of input dataset, you can ignore this
+# variable.
+#
+# The values can be any string to identify different parts of a survey
+# separated by white space characters (for example `f125w f160w' or `J
+# H' if you want to specify two filters).
+#
+# To be clean and also help in readability of the pipeline, it is good
+# practice to define a separate `filter-XXXX' variable for each
+# survey/dataset, even if they have overlapping filters.
+#
+# These `filters' are used in the initial downloading of the data and
+# it is good practice (for avoiding bugs) to keep the same filter (and
+# survey) names in the filenames of the intermediate/output files
+# also. This will make sure that the raw input and intermediate/final
+# output are exactly related.
+filters-survey = a b c d e f g h i
diff --git a/reproduce/config/pipeline/pdf.mk b/reproduce/config/pipeline/pdf.mk
new file mode 100644
index 0000000..51ab933
--- /dev/null
+++ b/reproduce/config/pipeline/pdf.mk
@@ -0,0 +1,14 @@
+# Make the final PDF?
+# -------------------
+#
+# During the testing a pipeline, it is usually not necessary to build
+# the PDF file (which makes a lot of output lines on the command-line
+# and can make it hard to find the commands and possible errors (and
+# their outputs). Also, in some cases, only the produced results may
+# be of interest and not the final PDF, so LaTeX (and its necessary
+# packages) may not be installed.
+#
+# If this variable is given any string, a PDF will be made with
+# LaTeX. Otherwise, a notice will just printed that for now, no PDF
+# will be created.
+pdf-compile = yes
diff --git a/reproduce/config/pipeline/web.mk b/reproduce/config/pipeline/web.mk
new file mode 100644
index 0000000..f80b886
--- /dev/null
+++ b/reproduce/config/pipeline/web.mk
@@ -0,0 +1,6 @@
+# Web server(s) hosting the input data for this pipeline.
+#
+# This is the web page containing the files that must be located in the
+# `SURVEY' directory of `reproduce/config/pipeline/DIRECTORIES.mk' on the
+# local system.
+web-survey = https://some.webpage.com/example/server
diff --git a/reproduce/src/make/download.mk b/reproduce/src/make/download.mk
new file mode 100644
index 0000000..244bd04
--- /dev/null
+++ b/reproduce/src/make/download.mk
@@ -0,0 +1,68 @@
+# Download all the necessary inputs if they are not already present.
+#
+# Since most systems only have one input/connection into the network,
+# downloading is essentially a serial (not parallel) operation. so the
+# recipes in this Makefile all use a single file lock to have one download
+# script running at every instant.
+#
+# Original author:
+#     Your name <your@email.address>
+# Contributing author(s):
+# Copyright (C) YYYY, Your Name.
+#
+# This Makefile is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details. See <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# Identify the downloader tool
+# ----------------------------
+#
+# If cURL is already present, that will be used, otherwise, we'll use
+# Wget. Since the options specifying the output filename are different
+# between the two, we'll also specify the output option within the
+# `downloader' variable. So it is important to first give the output
+# filename after calling `downloader', then the web address.
+downloader := $(shell if type curl > /dev/null; then downloader="curl -o";  \
+	              else                           downloader="wget -O";  \
+	              fi; echo "$$downloader";                               )
+
+
+
+
+
+# Download SURVEY data
+# --------------------
+#
+# Data from a survey (for example an imaging survey) usually have a special
+# file-name format which should be set here in the `foreach' loop. Note
+# that the `foreach' function needs the backslash (`\') at the end of the
+# line when it is broken into multiple lines.
+all-survey = $(foreach f, $(filters-survey),                                 \
+                          $(SURVEY)/a-special-format-$(f).fits               \
+                          $(SURVEY)/a-possibly-additional-$(f)-format.fits )
+$(SURVEY):; mkdir $@
+$(all-survey): $(SURVEY)/%: | $(SURVEY) $(lockdir)
+	flock $(lockdir)/download -c "$(downloader) $@ $(web-survey)/$*"
+
+
+
+
+
+
+# Final TeX macro
+# ---------------
+#
+# It is very important to mention the address where the data were
+# downloaded in the final report.
+$(mtexdir)/download.tex: $(pconfdir)/web.mk | $(mtexdir)
+	@echo "\\newcommand{\\websurvey}{$(web-survey)}" > $@
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
new file mode 100644
index 0000000..2da5e79
--- /dev/null
+++ b/reproduce/src/make/initialize.mk
@@ -0,0 +1,114 @@
+# Initialize the reproduction pipeline.
+#
+# Original author:
+#     Your name <your@email.address>
+# Contributing author(s):
+# Copyright (C) YYYY, Your Name.
+#
+# This Makefile is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# High-level directory definitions
+# --------------------------------
+#
+# Basic directories that are used throughout the whole pipeline.
+#
+# Locks are used to make sure that an operation is done in series not in
+# parallel (even if Make is run in parallel with the `-j' option). The most
+# common case is downloads which are better done in series and not in
+# parallel. Also, some programs may not be thread-safe, therefore it will
+# be necessary to put a lock on them. This pipeline uses the `flock'
+# program to achieve this.
+texdir = $(BDIR)/tex
+lockdir = $(BDIR)/locks
+bdirsym = reproduce/build
+mtexdir = $(texdir)/macros
+pconfdir = reproduce/config/pipeline
+
+
+
+
+
+# Make the high-level level directories
+# ------------------------------
+#
+# These are just the top-level directories for all the separate steps. The
+# directories (or possible sub-directories) for individual steps will be
+# defined and added within their own Makefiles.
+$(BDIR):; mkdir $@;
+$(mtexdir): | $(texdir); mkdir $@
+$(texdir) $(lockdir): | $(BDIR); mkdir $@
+
+
+
+
+
+# High-level Makefile management
+# ------------------------------
+#
+# About `.PHONY': these are targets that must be built even if a file with
+# their name exists. Most don't correspond to a file, but those that do are
+# included here ensure that the file is always built in every run: for
+# example the pipeline versions may change within two separate runs, so we
+# want it to be rebuilt every time.
+.PHONY: all clean clean-mmap $(texdir)/versions.tex
+clean-mmap:; rm -f reproduce/config/gnuastro/mmap*
+clean:
+	rm -rf $(BDIR) $(bdirsym) *.pdf *.log *.out *.aux *.auxlock \
+               reproduce/config/gnuastro/mmap*
+
+
+
+
+
+# Pipeline version
+# ----------------
+#
+# The pipeline's version is necessary for the analysis and must be
+# calculated everytime the pipeline is run, so even though this file
+# actually exists, it is also aded as a `.PHONY' target above.
+$(mtexdir)/initialize.tex: | $(mtexdir)
+
+	@v=$$(git describe --dirty --always);                      \
+	echo "\newcommand{\pipelineversion}{$$v}"  > $@
+
+	@v=$$(astnoisechisel --version | awk 'NR==1{print $$NF}'); \
+	echo "\newcommand{\gnuastroversion}{$$v}" >> $@
+
+	echo "\newcommand{\bdir}{$(BDIR)}" >> $@
+
+
+
+
+
+# Symbolic link to build directory
+# --------------------------------
+#
+# Besides $(BDIR), we are also making a symbolic link to it if $(bdirsym)
+# is not empty. In case this symbolic link is not needed, simply remove its
+# value from the definitions above. In that case, it will be read as a
+# blank (non-existant).
+#
+# Note that $(BDIR) might not be an absolute path and this will complicate
+# the symbolic link creation. To be generic, we'll first call `readlink' to
+# make sure we have an absolute address, then we'll make a symbolic link to
+# that.
+ifneq ($(bdirsym),)
+$(bdirsym): | $(BDIR)
+	absbdir=$$(readlink -f $(BDIR));                        \
+	ln -s $$absbdir $(bdirsym)
+endif
diff --git a/reproduce/src/make/paper.mk b/reproduce/src/make/paper.mk
new file mode 100644
index 0000000..0725ec8
--- /dev/null
+++ b/reproduce/src/make/paper.mk
@@ -0,0 +1,34 @@
+# Build the final PDF paper/report.
+#
+# Original author:
+#     Your name <your@email.address>
+# Contributing author(s):
+# Copyright (C) YYYY, Your Name.
+#
+# This script is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This script is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# The final paper
+# ---------------
+#
+# The commands to build the final report. We want the pipeline version to
+# be checked everytime the final PDF is to be built.
+paper.pdf: tex/pipeline.tex paper.tex
+
+        # Make the report.
+	@pdflatex -shell-escape -halt-on-error paper.tex
+	@rm -f *.auxlock *.aux *.out *.log
diff --git a/tex/preamble-biblatex.tex b/tex/preamble-biblatex.tex
new file mode 100644
index 0000000..757f007
--- /dev/null
+++ b/tex/preamble-biblatex.tex
@@ -0,0 +1,115 @@
+%% Biblatex settings.
+%%
+%% Since the preamble settings necessary to make the bibliography with
+%% Biblatex is a little long and unclean, and might be used in other places
+%% separately later, it is easier to have it here as a separate file.
+%%
+%% USAGE:
+%%
+%%  - `tex/ref.tex': the file containing Bibtex source of each
+%%     reference. The file suffix doesn't have to be `.bib', this naming
+%%     helps in clearly identifying the files and avoiding places that
+%%     complain about `.bib' files.
+
+
+
+
+
+%% To break up highlighted text (for example texttt when some it is on the
+%% line break) and also to no underline emphasized words (like journal
+%% titles in the references).
+\usepackage[normalem]{ulem}
+
+
+
+
+
+% Basic BibLaTeX settings
+\usepackage[
+    doi=false,
+    url=false,
+    dashed=false,
+    eprint=false,
+    maxbibnames=4,
+    minbibnames=1,
+    hyperref=true,
+    maxcitenames=2,
+    mincitenames=1,
+    style=authoryear,
+    uniquelist=false,
+    backend=biber,natbib]{biblatex}
+\DeclareFieldFormat[article]{pages}{#1}
+\DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
+\addbibresource{./tex/ref.tex}
+\renewbibmacro{in:}{}
+\renewcommand*{\bibfont}{\footnotesize}
+\DefineBibliographyStrings{english}{references = {References}}
+
+%% Include the adsurl field key into those that are recognized:
+\DeclareSourcemap{
+  \maps[datatype=bibtex]{
+    \map{
+      \step[fieldsource=adsurl,fieldtarget=iswc]
+      \step[fieldsource=gbkurl,fieldtarget=iswc]
+    }
+  }
+}
+
+%% Set the color of the doi link to mymg (magenta) and the ads links
+%% to mypurp (or purple):
+\definecolor{mypurp}{cmyk}{0.75,1,0,0}
+\newcommand{\doihref}[2]{\href{#1}{\color{magenta}{#2}}}
+\newcommand{\adshref}[2]{\href{#1}{\color{mypurp}{#2}}}
+\newcommand{\blackhref}[2]{\href{#1}{\color{black}{#2}}}
+
+%% Define a format for the printtext commands in
+%% DeclareBibliographyDriver to make links for the doi, ads link and
+%% arxiv link:
+\DeclareFieldFormat{doilink}{
+  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
+\DeclareFieldFormat{adslink}{
+    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
+\DeclareFieldFormat{arxivlink}{
+  \iffieldundef{eprint}{#1}{\href{http://arxiv.org/abs/\thefield{eprint}}{#1}}}
+
+\DeclareListFormat{doiforbook}{
+  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
+\DeclareFieldFormat{googlebookslink}{
+    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
+
+%% Set the formatting to make the last three values into the
+%% appropriate link. Note that the % signs are necessary. Without
+%% them, the items will be indented.
+\DeclareBibliographyDriver{article}{%
+  \usebibmacro{bibindex}%
+  \usebibmacro{begentry}%
+  \usebibmacro{author/translator+others}%
+  \newunit%
+  \ifdefined\makethesis\printtext{\usebibmacro{title}}\fi%
+  \newunit%
+  \printtext[doilink]{\usebibmacro{journal}}%
+  \addcomma%
+  \printtext[adslink]{\printfield{volume}}%
+  \addcomma%
+  \printtext[arxivlink]{\printfield{pages}}%
+  \addperiod%
+}
+
+\DeclareBibliographyDriver{book}{%
+  \usebibmacro{bibindex}%
+  \usebibmacro{begentry}%
+  \usebibmacro{author/translator+others}%
+  \newunit%
+  \printtext{\usebibmacro{title}}%
+  \addperiod%
+  \addspace%
+  \printlist[doiforbook]{publisher}%
+  \addcomma%
+  \addspace%
+  \printfield[googlebookslink]{edition}%
+  \printtext{ ed.}%
+  \addperiod%
+}
+
+%% In order to have et al. instead of et al.,:
+\renewcommand*{\nameyeardelim}{\addspace}
diff --git a/tex/preamble-necessary.tex b/tex/preamble-necessary.tex
new file mode 100644
index 0000000..debcb4b
--- /dev/null
+++ b/tex/preamble-necessary.tex
@@ -0,0 +1,68 @@
+%% Some (commonly) necessary LaTeX packages.
+%%
+%% These are a set of packages that are commonly necessary in most LaTeX
+%% usages. However, if any are not needed in your work, you can remove them
+%% from here.
+
+
+
+
+
+% Macros for to help in typing, remove them if you don't need them, but
+% this can help as a demo on how you can simply writing of commonly used
+% words that need special formatting (like software names).
+\newcommand{\snsign}{{\small S}/{\small N}}
+\newcommand{\originsoft}{\textsf{ORIGIN}}
+\newcommand{\sextractor}{\textsf{SE\-xtractor}}
+\newcommand{\noisechisel}{\textsf{Noise\-Chisel}}
+\newcommand{\makecatalog}{\textsf{Make\-Catalog}}
+
+
+
+
+
+%% For highlighting updates. When this is set, text marked as \new
+%% will be colored in dark green and text that is marked wtih \tonote
+%% will be marked in dark red.
+\ifdefined\highlightchanges
+\newcommand{\new}[1]{\textcolor{green!60!black}{#1}}
+\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}}
+\else
+\newcommand{\new}[1]{\textcolor{black}{#1}}
+\newcommand{\tonote}[1]{{}}
+\fi
+
+
+
+
+
+% Better than verbatim for displaying typed text.
+\usepackage{alltt}
+
+
+
+
+
+% For arithmetic opertions within LaTeX
+\usepackage[nomessages]{fp}
+
+
+
+
+
+%To add a code font to the text:
+\usepackage{courier}
+
+
+
+
+
+%To add some enumerating styles
+\usepackage{enumerate}
+
+
+
+
+
+%Including images if necessary
+\usepackage{graphicx}
diff --git a/tex/preamble-pgfplots.tex b/tex/preamble-pgfplots.tex
new file mode 100644
index 0000000..13570e9
--- /dev/null
+++ b/tex/preamble-pgfplots.tex
@@ -0,0 +1,33 @@
+%% PGFPlots settings.
+%%
+%% PGFPlots is a package in (La)TeX for making plots internally. It fits
+%% nicely with the purpose of a reproduction pipeline. But it isn't
+%% mandatory. Therefore if needed, you can just uncomment the line that
+%% includes this file in the top LaTeX source (`paper.tex').
+
+
+
+
+
+% For a tikz environment:
+\usepackage{tikz}
+\usetikzlibrary{external}
+\tikzexternalize
+
+\tikzsetexternalprefix{\bdir/tex/tikz/}
+
+%% Uncomment the following lines for EPS and PS images. Note that you
+%% still have to use pdflatex and also add a `[dvips]' option to
+%% graphicx.
+
+%\tikzset{external/system call={rm -f "\image".eps "\image".ps
+%"\image".dvi; latex \tikzexternalcheckshellescape -halt-on-error
+%-interaction=batchmode -jobname "\image" "\texsource";
+%dvips -o "\image".ps "\image".dvi;
+%ps2eps "\image.ps"}}
+
+%For drawing plots:
+\usepackage{pgfplots}
+\pgfplotsset{compat=newest}
+\usepgfplotslibrary{groupplots}
+\pgfplotsset{axis line style={thick}, tick style={semithick}}
diff --git a/tex/preamble-style.tex b/tex/preamble-style.tex
new file mode 100644
index 0000000..ae7ce92
--- /dev/null
+++ b/tex/preamble-style.tex
@@ -0,0 +1,97 @@
+%% General paper's style settings.
+%%
+%% This preamble can be completely ignored when including this TeX file in
+%% another style. This is done because this LaTeX build is meant to be an
+%% initial/internal phase or part of a larger effort, so it has a basic
+%% style defined here as a preamble. To ignore it, uncomment or delete the
+%% respective line in `paper.tex'.
+
+
+
+%% Print size
+\usepackage[a4paper, includeheadfoot, body={18.7cm, 24.5cm}]{geometry}
+
+
+
+
+%% Set the distance between the columns if two columns:
+\setlength{\columnsep}{0.75cm}
+
+
+
+
+
+% To allow figures to take up more space on the top of the page:
+\renewcommand{\topfraction}{.99}
+\renewcommand{\bottomfraction}{.7}
+\renewcommand{\textfraction}{.05}
+\renewcommand{\floatpagefraction}{.99}
+\renewcommand{\dbltopfraction}{.99}
+\renewcommand{\dblfloatpagefraction}{.99}
+\setcounter{topnumber}{1}
+\setcounter{bottomnumber}{0}
+\setcounter{totalnumber}{2}
+\setcounter{dbltopnumber}{1}
+
+
+
+%% Color related settings:
+\usepackage{xcolor}
+\color{black}                   % Text color
+\definecolor{DarkBlue}{RGB}{0,0,90}
+
+
+% figure and figure* ordering correction:
+\usepackage{fixltx2e}
+
+
+
+%% For editing the caption appearence. The `setspace' package defines
+%% the `stretch' variable. `abovecaptionskip' is the distance between
+%% the figure and the caption.
+\usepackage{setspace, caption}
+\captionsetup{font=small, labelfont={color=DarkBlue,bf}, skip=1pt}
+\captionsetup[figure]{font={stretch=1, small}}
+\setlength{\abovecaptionskip}{3pt plus 1pt minus 1pt}
+
+
+
+%% To make the footnotes align:
+\usepackage[hang]{footmisc}
+\setlength\footnotemargin{10pt}
+
+
+
+%For including time in the title:
+\usepackage{datetime}
+
+
+
+%To make links to webpages and include document information in the
+%properties of the PDF
+\usepackage[
+  colorlinks,
+  urlcolor=blue,
+  citecolor=blue,
+  linkcolor=blue,
+  linktocpage]{hyperref}
+\renewcommand\UrlFont{\rmfamily}
+
+
+
+% Basic Document information
+\hypersetup
+{
+    pdfauthor={Mohammad Akhlaghi},
+    pdfsubject={MUSE detected objects},
+    pdftitle={Broadband HST photometry of MUSE detected objects},
+    pdfkeywords={Mohammad, Akhlaghi, photometry, MUSE, HST}
+}
+
+
+
+% Title
+\title{A nice title for your research project}
+\date{\small Reproduction pipeline \pipelineversion{}
+      and Gnuastro \gnuastroversion\\on \today, \currenttime}
+\author{Your name here.}